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I had the same question back when I started the UUV simulator. In the end the decision was to publish a world ned frame and use it as a reference frame. At least from the simulation point of view, I modified the sensor plugins so that they could use both world and world_ned frames, and the vehicles also have base_link and base_link_ned (as in this example here). I am not sure if this is the best/easiest approach, but I couldn't find many other references in this subject.